geuvadis_rnaseq

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97 discussions

Re: [Geuvadis_rnaseq] Minutes Geuvadis RNAseq TC on May 6

by Gabrielle Anne Bertier

Dear Thomas, thank you very much for these minutes. I would like to remind you all that our first official deliverable for WP4, D4.1 due on November 2011 is the following: Database for RNAseq pilot project. Also due in November 2011 are the following Milestones MS10 Database established and functional for pilot project. MS11 Selection of pilot samples completed. Find below a description of the first task of the WP as in the Grant Agreement. Kind regards, Gabrielle Task 4.1 RNA sequencing in 500 pilot samples For the pilot RNA sequencing project, samples will be selected from the set of individuals that have been selected for exon resequencing in WP5. RNAseq will be performed with standard protocols as described by Mortazavi et al. (Nature Methods 2008). Each RNA sample will be sequenced at a depth of at least 20 million reads with a paired end protocol. Coordination of data processing, data sharing and data analysis will be modelled using this dataset. We are in the process of piloting this approach by RNAseq of the same 5 RNA samples from individuals of the CEU panel of the HapMap3 and 1000GP projects in 8 different sequencing centres across Europe. The data has been produced and we are in the process of finalizing the plans for centralized deposit of the data and joint analysis. A database for samples and clinical data sets will be implemented (WP3) to facilitate the project and to monitor its progress (WP1). A web-based service will enable both project partners and external collaborators to enter all information relevant for the project. Completed entries will be required for samples participating in the pilot project. The structure of the databases will be such that will facilitate the deposit of various types of functional genomics datasets such as ChIPseq, GROseq, and methylation-seq. Gabrielle Bertier Project Manager International Collaboration and Sponsorship Office CRG, Center for Genomic Regulation Carrer Dr. Aiguader, 88 08003 Barcelona, España Tel: +34933160374 Mobile: +34639960656 email: gabrielle.bertier(a)crg.es<mailto:gabrielle.bertier@crg.es> web: www.geuvadis.eu -----Original Message----- From: geuvadis_rnaseq-bounces(a)lists.crg.es [mailto:geuvadis_rnaseq-bounces@lists.crg.es] On Behalf Of Thomas Giger Sent: viernes, 06 de mayo de 2011 15:48 To: geuvadis_rnaseq(a)lists.crg.es Subject: [Geuvadis_rnaseq] Minutes Geuvadis RNAseq TC on May 6 Dear All, thanks a lot for participating in the TC today. Please find attached to this message a word document containing the minutes of the particular points that were discussed. This document contains very important information on changes of the experimental design - please read it. Please don't hesitate to ask me if I am unclear or if I missed something. cheers, Thomas

13 years, 4 months

[Geuvadis_rnaseq] Minutes Geuvadis RNAseq TC on May 6

by Thomas Giger

Dear All, thanks a lot for participating in the TC today. Please find attached to this message a word document containing the minutes of the particular points that were discussed. This document contains very important information on changes of the experimental design - please read it. Please don't hesitate to ask me if I am unclear or if I missed something. cheers, Thomas ------------------------------------------------------------------------ Thomas Giger, Ph.D. Department of Genetic Medicine and Development University of Geneva Medical School 1 Rue Michel-Servet Geneva 1211 Switzerland

13 years, 4 months

[Geuvadis_rnaseq] conference call

by Matthias Barann

Dear all, just to let you know, I'm experiencing some difficulties getting into the conference. For whatever reason the PIN is not accepted. I can't get into contact with an operator either. We're still trying, but I can't promise we can fix this in time. best regards, Matthias Barann

13 years, 4 months

[Geuvadis_rnaseq] Geuvadis RNAseq TC details

by Thomas Giger

Dear All, thank you for having filled in the doodle. The Geuvadis RNAseq phone conference will take place on May 6 from 11am - 12pm CEST. To participate in this call you have to do the following: - if you call in from Switzerland dial: +41 58 262 07 22 - otherwise from other countries please find enclosed the list with the "local access numbers for teleconferences" and dial the number corresponding to your country. Then enter the PIN: 611683 In case you need assistance during the call - dial "OO" (nil nil) to get in touch with an operator. I have written down the following points that should be discussed: 1. As of now we made plans that the different labs analyze samples from one particular population (as listed in the workflow document that I've sent around on April 7). It would be a better experimental design if the samples were randomly distributed among the different labs. Since there is still time to react - do we want to switch the strategy? 2. How long are the library prep / sequencer queue up times in the different labs (once you receive the RNA samples - how long do you think will it take you to analyze them?). If some labs expect to have much larger delays, we could make arrangements that those labs get samples earlier than other labs. This would also mean that we would all use the protocol that is used at the time point when the first lab starts to analyze samples. 3. Which other samples (other than the 500 1KGP European samples) should be analyzed by RNAseq? 4. Specifications for the small RNA protocol. If you already know now, that you would like to have additional things discussed - please let me know and I can make sure that we don't forget about. Looking forward to talk to you soon, Thomas ------------------------------------------------------------------------ Thomas Giger, Ph.D. Department of Genetic Medicine and Development University of Geneva Medical School 1 Rue Michel-Servet Geneva 1211 Switzerland

13 years, 4 months

[Geuvadis_rnaseq] reminder Geuvadis TC tomorrow 11am

by Thomas Giger

Dear All, This message is a reminder for the Geuvadis RNAseq phone conference that will take place tomorrow May 6 from 11am - 12pm CEST. Here again the most important information for this call (the same information as in my mail from April 26): To participate in this call you have to do the following: - if you call in from Switzerland dial: +41 58 262 07 22 - otherwise from other countries please find enclosed the list with the "local access numbers for teleconferences" and dial the number corresponding to your country. Then enter the PIN: 611683 In case you need assistance during the call - dial "OO" (nil nil) to get in touch with an operator. I have written down the following points that should be discussed: 1. As of now we made plans that the different labs analyze samples from one particular population (as listed in the workflow document that I've sent around on April 7). It would be a better experimental design if the samples were randomly distributed among the different labs. Since there is still time to react - do we want to switch the strategy? 2. How long are the library prep / sequencer queue up times in the different labs (once you receive the RNA samples - how long do you think will it take you to analyze them?). If some labs expect to have much larger delays, we could make arrangements that those labs get samples earlier than other labs. This would also mean that we would all use the protocol that is used at the time point when the first lab starts to analyze samples. 3. Which other samples (other than the 500 1KGP European samples) should be analyzed by RNAseq? 4. Specifications for the small RNA protocol. Looking forward to talk to you tomorrow, Thomas ------------------------------------------------------------------------ Thomas Giger, Ph.D. Department of Genetic Medicine and Development University of Geneva Medical School 1 Rue Michel-Servet Geneva 1211 Switzerland

13 years, 4 months

[Geuvadis_rnaseq] RNAseq TC

by Thomas Giger

Dear All, As we decided yesterday, the people involved in the RNAseq related part of the experiment should have a conference call to discuss open questions. I have written down the following points that should be discussed: 1. As of now we made plans that the different labs analyze samples from one particular population (as listed in the workflow document that I've sent around on April 7). It would be a better experimental design if the samples were randomly distributed among the different labs. Since there is still time to react - do we want to switch the strategy? 2. How long are the library prep / sequencer queue up times in the different labs (once you receive the RNA samples - how long do you think will it take you to analyze them?). If some labs expect to have much larger delays, we could make arrangements that those labs get samples earlier than other labs. This would also mean that we would all use the protocol that is used at the time point when the first lab starts to analyze samples. 3. Which other samples (other than the 500 1KGP European samples) should be analyzed by RNAseq? 4. Specifications for the small RNA protocol. If you know already now, that you would like to have additional things discussed - please let me know and I can make sure that we don't forget about. We would like to schedule the call for either next Tuesday (April 26) or Wednesday (April 27). Please fill in the doodle by the end of this week so that we can select a time where a maximum number of people can attend the call: http://doodle.com/cnfc85cx9ushxzyb cheers, Thomas ------------------------------------------------------------------------ Thomas Giger, Ph.D. Department of Genetic Medicine and Development University of Geneva Medical School 1 Rue Michel-Servet Geneva 1211 Switzerland

13 years, 5 months

[Geuvadis_rnaseq] RNAseq Sample Workflow

by geuvadis_rnaseq＠lists.crg.es

From: Thomas Giger <Thomas.Giger(a)unige.ch<mailto:Thomas.Giger@unige.ch>> Date: April 7, 2011 10:11:26 AM GMT+02:00 To: geuvadis_rnaseq(a)lists.crg.es<mailto:geuvadis_rnaseq@lists.crg.es> Subject: RNAseq Sample Workflow Dear All, please find attached to this message the sample processing workflow. If something is unclear - please don't hesitate to ask me. Also we could discuss this workflow further during the next TC. kindest regards, Thomas

13 years, 5 months

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